>What codepoint should be used to encode the letter which later seperated
>into U/V?

U+0055 (U), I would have thought, since this is the vowel that is descended
directly from the Latin and which is used in most transcriptions of Latin
texts. If you want your text to 'look' Latin -- e.g. to emulate a Roman
inscription -- then you might use V, but your text would no longer be
spelled correctly (does anyone have a Latin spellchecker?).

The elegant solution would be to use an OpenType font with a glyph
substitution lookup that would 'Romanise' the rendering of your text but
retain the correct backing string.